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Article: Retrospective Phylodynamic and Phylogeographic Analysis of the Human Papillomavirus 16 E6 Gene in the Mediterranean Region.

Souiai, Oussama / Sallemi, Ameni

2023 Volume 17, Page(s) 11779322231178598

Abstract: Human papillomavirus 16 (HPV16) is considered to be strongly correlated with the development of cervical cancer. Among the 8 HPV16 genes, the E6 constitutes a remarkable marker to follow the evolutionary history and spatial phylodynamics of HPV16 in the ... ...

Abstract	Human papillomavirus 16 (HPV16) is considered to be strongly correlated with the development of cervical cancer. Among the 8 HPV16 genes, the E6 constitutes a remarkable marker to follow the evolutionary history and spatial phylodynamics of HPV16 in the Mediterranean basin. Thus, this work aims to decipher the major evolutionary events and crosstalks in the Mediterranean basin with a focus on Tunisian strains regarding the E6 oncogene. In this study, we first extracted the available and annotated Mediterranean strains of HPV16 E6 gene sequences (n = 155) from the NCBI nucleotide database. These sequences were aligned, edited, and used for the downstream phylogenetic analyses. Finally, a Bayesian Markov Chain Monte Carlo approach was applied to reconstruct the evolutionary history of HPV16 migration. Our results showed that the HPV circulating in Tunisia derived from a Croatian ancestor around the year 1987. This starting point spreads to most European countries to reach northern Africa through the Moroccan gateway in 2004.
Language	English
Publishing date	2023-06-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	2423808-9
ISSN	1177-9322
ISSN	1177-9322
DOI	10.1177/11779322231178598
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Article: Applied Machine Learning Toward Drug Discovery Enhancement: Leishmaniases as a Case Study.

Harigua-Souiai, Emna / Oualha, Rafeh / Souiai, Oussama / Abdeljaoued-Tej, Ines / Guizani, Ikram

Bioinformatics and biology insights

2022 Volume 16, Page(s) 11779322221090349

Abstract: Drug discovery (DD) research is a complex field with a high attrition rate. Machine learning (ML) approaches combined to chemoinformatics are of valuable input to this field. We, herein, focused on implementing multiple ML algorithms that shall learn ... ...

Abstract	Drug discovery (DD) research is a complex field with a high attrition rate. Machine learning (ML) approaches combined to chemoinformatics are of valuable input to this field. We, herein, focused on implementing multiple ML algorithms that shall learn from different molecular fingerprints (FPs) of 65 057 molecules that have been identified as active or inactive against
Language	English
Publishing date	2022-04-22
Publishing country	United States
Document type	Journal Article
ZDB-ID	2423808-9
ISSN	1177-9322
ISSN	1177-9322
DOI	10.1177/11779322221090349
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Article ; Online: Phylogeographic Dynamics of H9N2 Avian Influenza Viruses in Tunisia.

Larbi, Imen / Arbi, Marwa / Souiai, Oussama / Tougorti, Halima / Butcher, Gary David / Nsiri, Jihene / Badr, Chaima / Behi, Imen El / Lachhab, Jihene / Ghram, Abdeljelil

Virus research

2024 Volume 344, Page(s) 199348

Abstract: Avian influenza virus subtype H9N2 is endemic in commercial poultry in Tunisia. This subtype affects poultry and wild birds in Tunisia and poses a potential zoonotic risk. Tunisian H9N2 strains carry, in their hemagglutinins, the human-like marker 226 L ... ...

Abstract	Avian influenza virus subtype H9N2 is endemic in commercial poultry in Tunisia. This subtype affects poultry and wild birds in Tunisia and poses a potential zoonotic risk. Tunisian H9N2 strains carry, in their hemagglutinins, the human-like marker 226 L that is most influential in avian-to-human viral transmission. For a better understanding of how ecological aspects of the H9N2 virus and its circulation in poultry, migratory birds and environment shapes the spread of the dissemination of H9N2 in Tunisia, herein, we investigate the epidemiological, evolutionary and zoonotic potential of seven H9N2 poultry isolates and sequence their whole genome. Phylogeographic and phylodymanic analysis were used to examine viral spread within and among wild birds, poultry and environment at geographical scales. Genetic evolution results showed that the eight gene sequences of Tunisian H9N2 AIV were characterized by molecular markers involved with virulence and mammalian infections. The geographical distribution of avian influenza virus appears as a network interconnecting countries in Europe, Asia, North Africa and West Africa. The spatiotemporal dynamics analysis showed that the H9N2 virus was transmitted from Tunisia to neighboring countries notably Libya and Algeria. Interestingly, this study also revealed, for the first time, that there was a virus transmission between Tunisia and Morocco. Bayesian analysis showed exchanges between H9N2 strains of Tunisia and those of the Middle Eastern countries, analysis of host traits showed that duck, wild birds and environment were ancestry related to chicken. The subtypes phylodynamic showed that PB1 segment was under multiple inter-subtype reassortment events with H10N7, H12N5, H5N2 and H6N1 and that PB2 was also a subject of inter-subtype reassortment with H10N4.
MeSH term(s)	Animals ; Influenza A Virus, H9N2 Subtype/genetics ; Influenza A Virus, H9N2 Subtype/classification ; Influenza A Virus, H9N2 Subtype/isolation & purification ; Tunisia/epidemiology ; Influenza in Birds/virology ; Influenza in Birds/epidemiology ; Influenza in Birds/transmission ; Phylogeography ; Phylogeny ; Poultry/virology ; Evolution, Molecular ; Poultry Diseases/virology ; Poultry Diseases/epidemiology ; Genome, Viral ; Animals, Wild/virology ; Birds/virology ; Chickens/virology
Language	English
Publishing date	2024-03-28
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	605780-9
ISSN	1872-7492 ; 0168-1702
ISSN (online)	1872-7492
ISSN	0168-1702
DOI	10.1016/j.virusres.2024.199348
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Article: Epidemiological and Phylogeographic Study of Equid Herpesviruses in Tunisia.

Badr, Chaima / Souiai, Oussama / Arbi, Marwa / El Behi, Imen / Essaied, Mohamed S / Khosrof, Ines / Benkahla, Alia / Chabchoub, Ahmed / Ghram, Abdeljelil

Pathogens (Basel, Switzerland)

2022 Volume 11, Issue 9

Abstract: Equid herpesvirus (EHV) is a contagious viral disease affecting horses, causing illness characterized by respiratory symptoms, abortion and neurological disorders. It is common worldwide and causes severe economic losses to the equine industry. The ... ...

Abstract	Equid herpesvirus (EHV) is a contagious viral disease affecting horses, causing illness characterized by respiratory symptoms, abortion and neurological disorders. It is common worldwide and causes severe economic losses to the equine industry. The present study was aimed at investigating the incidence of EHVs, the genetic characterization of Tunisian isolates and a spatiotemporal study, using 298 collected samples from diseased and clinically healthy horses. The global incidence of EHV infection was found to be about 71.81%. EHV2 and EHV5 were detected in 146 (48.99%) and 159 (53.35%) sampled horses, respectively. EHV1 was detected in 11 samples (3.69%); EHV4 was not detected. Co-infections with EHV1-EHV2, EHV1-EHV5 and EHV2-EHV5 were observed in 0.33%, 1.34% and 31.54% of tested horses, respectively. Phylogenetic analyses showed that gB of EHV2 and EHV5 displays high genetic diversity with a nucleotide sequence identity ranging from 88 to 100% for EHV2 and 97.5 to 100% for EHV5. Phylogeography suggested Iceland and USA as the most likely countries of origin of the Tunisian EHV2 and EHV5 isolates. These viruses detected in Tunisia seemed to be introduced in the 2000s. This first epidemiological and phylogeographic study is important for better knowledge of the evolution of equid herpesvirus infections in Tunisia.
Language	English
Publishing date	2022-09-05
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2695572-6
ISSN	2076-0817
ISSN	2076-0817
DOI	10.3390/pathogens11091016
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Article: Epidemiological and Phylogeographic Study of Equid Herpesviruses in Tunisia

Badr, Chaima / Souiai, Oussama / Arbi, Marwa / El Behi, Imen / Essaied, Mohamed S. / Khosrof, Ines / Benkahla, Alia / Chabchoub, Ahmed / Ghram, Abdeljelil

Pathogens. 2022 Sept. 05, v. 11, no. 9

2022

Abstract	Equid herpesvirus (EHV) is a contagious viral disease affecting horses, causing illness characterized by respiratory symptoms, abortion and neurological disorders. It is common worldwide and causes severe economic losses to the equine industry. The present study was aimed at investigating the incidence of EHVs, the genetic characterization of Tunisian isolates and a spatiotemporal study, using 298 collected samples from diseased and clinically healthy horses. The global incidence of EHV infection was found to be about 71.81%. EHV2 and EHV5 were detected in 146 (48.99%) and 159 (53.35%) sampled horses, respectively. EHV1 was detected in 11 samples (3.69%); EHV4 was not detected. Co-infections with EHV1-EHV2, EHV1-EHV5 and EHV2-EHV5 were observed in 0.33%, 1.34% and 31.54% of tested horses, respectively. Phylogenetic analyses showed that gB of EHV2 and EHV5 displays high genetic diversity with a nucleotide sequence identity ranging from 88 to 100% for EHV2 and 97.5 to 100% for EHV5. Phylogeography suggested Iceland and USA as the most likely countries of origin of the Tunisian EHV2 and EHV5 isolates. These viruses detected in Tunisia seemed to be introduced in the 2000s. This first epidemiological and phylogeographic study is important for better knowledge of the evolution of equid herpesvirus infections in Tunisia.
Keywords	Herpesvirales ; genetic variation ; horses ; industry ; nucleotide sequences ; phylogeny ; phylogeography ; sequence analysis ; Iceland ; Tunisia
Language	English
Dates of publication	2022-0905
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2695572-6
ISSN	2076-0817
ISSN	2076-0817
DOI	10.3390/pathogens11091016
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Functional insights into human macrophage response against Scedosporium apiospermum and Scedosporium dehoogii.

Mahmoud, Dorra Elhaj / Hanachi, Mariem / Yaakoub, Hajar / Blanchard, Simon / Pignon, Pascale / Souiai, Oussama / Delneste, Yves / Bouchara, Jean-Philippe / Papon, Nicolas / Hérivaux, Anaïs

Cytokine

2023 Volume 172, Page(s) 156384

Abstract: Fungal infections caused by Scedosporium species are rising among immunocompromised and immunocompetent patients. Within the immunocompetent group, patients with cystic fibrosis (pwCF) are at high risk of developing a chronic airway colonization by these ...

Abstract	Fungal infections caused by Scedosporium species are rising among immunocompromised and immunocompetent patients. Within the immunocompetent group, patients with cystic fibrosis (pwCF) are at high risk of developing a chronic airway colonization by these molds. While S. apiospermum is one of the major species encountered in the lungs of pwCF, S. dehoogii has rarely been reported. The innate immune response is believed to be critical for host defense against fungal infections. However, its role has only recently been elucidated and the immune mechanisms against Scedosporium species are currently unknown. In this context, we undertook a comparative investigation of macrophage-mediated immune responses toward S. apiospermum and S. dehoogii conidia. Our data showed that S. apiospermum and S. dehoogii conidia strongly stimulated the expression of a set of pro-inflammatory cytokines and chemokines such as IL-1β, IL-8, IL-6 and TNFα. We demonstrated that S. dehoogii was more potent in stimulating the early release of pro-inflammatory cytokines and chemokines while S. apiospermum induced a late inflammatory response at a higher level. Flow cytometry analysis showed that M1-like macrophages were able to internalize both S. apiospermum and S. dehoogii conidia, with a similar intracellular killing rate for both species. In conclusion, these results suggest that M1-like macrophages can rapidly initiate a strong immune response against both S. apiospermum and S. dehoogii. This response is characterized by a similar killing of internalized conidia, but a different time course of cytokine production.
MeSH term(s)	Humans ; Scedosporium/metabolism ; Macrophages ; Mycoses ; Cytokines/metabolism ; Cystic Fibrosis ; Chemokines/metabolism
Chemical Substances	Cytokines ; Chemokines
Language	English
Publishing date	2023-10-11
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1018055-2
ISSN	1096-0023 ; 1043-4666
ISSN (online)	1096-0023
ISSN	1043-4666
DOI	10.1016/j.cyto.2023.156384
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Article: Deep Learning Algorithms Achieved Satisfactory Predictions When Trained on a Novel Collection of Anticoronavirus Molecules.

Harigua-Souiai, Emna / Heinhane, Mohamed Mahmoud / Abdelkrim, Yosser Zina / Souiai, Oussama / Abdeljaoued-Tej, Ines / Guizani, Ikram

Frontiers in genetics

2021 Volume 12, Page(s) 744170

Abstract: Drug discovery and repurposing against COVID-19 is a highly relevant topic with huge efforts dedicated to delivering novel therapeutics targeting SARS-CoV-2. In this context, computer-aided drug discovery is of interest in orienting the early high ... ...

Abstract	Drug discovery and repurposing against COVID-19 is a highly relevant topic with huge efforts dedicated to delivering novel therapeutics targeting SARS-CoV-2. In this context, computer-aided drug discovery is of interest in orienting the early high throughput screenings and in optimizing the hit identification rate. We herein propose a pipeline for Ligand-Based Drug Discovery (LBDD) against SARS-CoV-2. Through an extensive search of the literature and multiple steps of filtering, we integrated information on 2,610 molecules having a validated effect against SARS-CoV and/or SARS-CoV-2. The chemical structures of these molecules were encoded through multiple systems to be readily useful as input to conventional machine learning (ML) algorithms or deep learning (DL) architectures. We assessed the performances of seven ML algorithms and four DL algorithms in achieving molecule classification into two classes: active and inactive. The Random Forests (RF), Graph Convolutional Network (GCN), and Directed Acyclic Graph (DAG) models achieved the best performances. These models were further optimized through hyperparameter tuning and achieved ROC-AUC scores through cross-validation of 85, 83, and 79% for RF, GCN, and DAG models, respectively. An external validation step on the FDA-approved drugs collection revealed a superior potential of DL algorithms to achieve drug repurposing against SARS-CoV-2 based on the dataset herein presented. Namely, GCN and DAG achieved more than 50% of the true positive rate assessed on the confirmed hits of a PubChem bioassay.
Language	English
Publishing date	2021-11-29
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2606823-0
ISSN	1664-8021
ISSN	1664-8021
DOI	10.3389/fgene.2021.744170
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Article: Genomic Characteristics of Invasive

Hanachi, Mariem / Kiran, Anmol / Cornick, Jennifer / Harigua-Souiai, Emna / Everett, Dean / Benkahla, Alia / Souiai, Oussama

Bioinformatics and biology insights

2020 Volume 14, Page(s) 1177932220962106

Abstract: Streptococcus ... ...

Abstract	Streptococcus pneumoniae
Language	English
Publishing date	2020-09-29
Publishing country	United States
Document type	Journal Article
ZDB-ID	2423808-9
ISSN	1177-9322
ISSN	1177-9322
DOI	10.1177/1177932220962106
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Article ; Online: Nuclear and mitochondrial genome sequencing of North-African

Bussotti, Giovanni / Benkahla, Alia / Jeddi, Fakhri / Souiaï, Oussama / Aoun, Karim / Späth, Gerald F / Bouratbine, Aïda

Microbial genomics

2020 Volume 6, Issue 10

Abstract: Although several studies have investigated genetic diversity ... ...

Abstract	Although several studies have investigated genetic diversity of
MeSH term(s)	Base Sequence ; Chromosome Mapping ; Comparative Genomic Hybridization ; Drug Resistance/genetics ; Genome, Mitochondrial/genetics ; Genome, Protozoan/genetics ; Geography ; Humans ; Leishmania infantum/genetics ; Leishmania infantum/isolation & purification ; Leishmaniasis, Visceral/epidemiology ; Mitochondria/genetics ; Sequence Alignment ; Tunisia/epidemiology ; Whole Genome Sequencing
Language	English
Publishing date	2020-11-20
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2835258-0
ISSN	2057-5858 ; 2057-5858
ISSN (online)	2057-5858
ISSN	2057-5858
DOI	10.1099/mgen.0.000444
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Article: Differential Gene Expression Patterns in Blood and Cerebrospinal Fluid of Multiple Sclerosis and Neuro-Behçet Disease.

Maghrebi, Olfa / Hanachi, Mariem / Bahrini, Khadija / Kchaou, Mariem / Jeridi, Cyrine / Belal, Samir / Ben Sassi, Samia / Barbouche, Mohamed-Ridha / Souiai, Oussama / Belghith, Meriam

Frontiers in genetics

2021 Volume 12, Page(s) 638236

Abstract: Inflammatory demyelinating disorders of the central nervous system are debilitating conditions of the young adult, here we focus on multiple sclerosis (MS) and neuro-Behçet disease (NBD). MS is an autoimmune disorder of the central nervous system. NBD, a ...

Abstract	Inflammatory demyelinating disorders of the central nervous system are debilitating conditions of the young adult, here we focus on multiple sclerosis (MS) and neuro-Behçet disease (NBD). MS is an autoimmune disorder of the central nervous system. NBD, a neurological manifestation of an idiopathic chronic relapsing multisystem inflammatory disease, the behçet disease. The diagnosis of MS and NBD relies on clinical symptoms, magnetic resonance imaging and laboratory tests. At first onset, clinical and imaging similarities between the two disorders may occur, making differential diagnosis challenging and delaying appropriate management. Aiming to identify additional discriminating biomarker patterns, we measured and compared gene expression of a broad panel of selected genes in blood and cerebrospinal fluid (CSF) cells of patients suffering from NBD, MS and non inflammatory neurological disorders (NIND). To reach this aim, bivariate and multivariate analysis were applied. The Principal Analysis Component (PCA) highlighted distinct profiles between NBD, MS, and controls. Transcription factors foxp3 in the blood along with IL-4, IL-10, and IL-17 expressions were the parameters that are the main contributor to the segregation between MS and NBD clustering. Moreover, parameters related to cellular activation and inflammatory cytokines within the CSF clearly differentiate between the two inflammatory diseases and the controls. We proceeded to ROC analysis in order to identify the most distinctive parameters between both inflammatory neurological disorders. The latter analysis suggested that IL-17, CD73 in the blood as well as IL-1β and IL-10 in the CSF were the most discriminating parameters between MS and NBD. We conclude that combined multi-dimensional analysis in blood and CSF suggests distinct mechanisms governing the pathophysiology of these two neuro-inflammatory disorders.
Language	English
Publishing date	2021-02-26
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2606823-0
ISSN	1664-8021
ISSN	1664-8021
DOI	10.3389/fgene.2021.638236
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